I had a file which had a lot of tileset work done in it, and so had gone through many modications over time. When saving/loading the file, it took an extremely long time.
However, all that was in the file now was a tile layer, and an empty layer. The saving time was quite extreme. Cropping the file did not change this, there was only frame, and it would still take a while to save if I re-opened it.
By copying the tile layer and pasting it into a new file, the save time was reduced to an instant despite resulting in an identical image.
So it seems as though there’s some data being saved which shouldn’t be, resulting in long load/save times.